Contemporary approaches to protein structure classification

BioEssays

Volumn 20, Issue 11, 1998, Pages 884-891

  Swindells, Mark B ^a,b   Orengo, Christine A ^e   Jones, David T ^c   Hutchinson, E Gail ^e   Thornton, Janet M ^d  

^a Helix Research Institute   (Japan)

^b Inpharmatica Ltd   (United Kingdom)

^c UNIVERSITY OF WARWICK   (United Kingdom)

^d UNIVERSITY OF LONDON   (United Kingdom)

^e NONE

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN DETECTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

EID: 0032213490     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-1878(199811)20:11<884::AID-BIES3>3.0.CO;2-H     Document Type: Review

References (53)

1. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, and Tasumi M (1977) The Protein Data Bank: A computer based archival file for macromolecular structures. J. Mol. Biol. 122:535-542.
2. Pastore A, and Lesk AM (1990) Comparison of globins and physocyanins: Evidence for evolutionary relationship. Proteins 8:133-155.
3. Holm L, and Sander C (1993) Globin fold in a bacterial toxin. Nature 361:309.
4. Swindells MB (1995) Identification of a common fold in the replication terminator protein suggests a possible mode for DNA binding. Trends in Bioc. Sci. 20:300-302.
5. Bussiere DE, Bastia D, and White SW (1995) Crystal structure of the replication terminator protein. Cell 80:651-660.
6. Ramakrishnan V, and Finch JT (1993) Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature 362:219-223.
7. Jones DT, Taylor WR, and Thornton JM (1992) A new approach to fold recognition. Nature 358:86-89.
8. Bowie JU, Lüthy R, and Eisenberg D (1991) A method to identify protein sequences that fold into a known three dimensional structure. Science 253:164-169.
9. Nishikawa K, and Matsuo Y (1993) Development of psuedoenergy potentials for assessing protein 3D-1D compatibility and detecting weak homologies. Prof. Eng. 6:811-820.
10. Flockner H, Braxenthaler M, Lackner-P Jartz-M, Ortner M, and Sippl MJ (1995) Progress in fold recognition. Proteins 23:376-386.
11. Fischer D, Rice D, Bowie JU, and Eisenberg D (1995) Assigning amino acid sequences to 3-dimensional protein folds. FASEB 10:126-136.
12. Sippl MJ, and Flockner H (1996) Threading thrills and threats. Structure 4:15-19.
13. Murzin AG, and Chothia C (1992) Protein architecture: new superfamilies. Curr. Opin. Struct. Biol. 2:895-903.
14. Swindells MB (1992) Structural similarity between transforming growth factor-β2 and nerve growth factor. Science 258:1160-1161.
15. Murzin AG (1996) Structural classification of proteins: new superfamilies. Curr. Opin. Struct. Biol. 6:386-394.
16. Karpen ME, de-Haseth PL, and Neet KE (1989) Comparing short protein substructures by a method based on backbone torsion angles. Proteins 6:155-67.
17. Matsuo Y, and Kanehisa M (1993) an approach to systematic detection of protein structural motifs. Comput. Appl. Biosci. 9:153-159.
18. Rossmann MG, and Argos P (1976) Exploring structural homology of proteins. J Mol. Biol. 105:75-95.
19. Vriend G, and Sander C. (1991) Detection of three dimensional substructures in proteins. Proteins 11:52-58.
20. Alexandrov NN, Takahashi K, and Go N (1992) Common spatial arrangements of backbone fragments in homologous and nonhomologous proteins. J. Mol. Biol. 225:5-9.
21. Taylor WH, and Orengo C (1989) Protein structure alignment. J. Mol. Biol. 208:1-22.
22. Orengo CA, Brown NP, and Taylor WR (1992) Fast structure alignment for protein databank searching. Proteins 14:139-167.
23. Orengo CA, and Taylor WR (1996) SSAP: Sequential structure alignment program for protein structure comparison. Methods Enzymol 266: 617-635.
24. Sali A, and Blundell TL (1990) The definition of general topological equivalence in protein structures: A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212:403-428.
25. Mitchell EM, Artymiuk PJ, Rice DW, and Willett DW (1989) Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J. Mol. Biol. 212:151-166.
26. Holm L, and Sander C (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:123-138.
27. Nussinov R, and Woolfson HJ (1989) Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl. Acad. Sci. 88:10495-10499.
28. Pascarella S, and Argos P (1992) A data bank merging related protein structures and sequences. Prot. Eng. 2:121-137.
29. Orengo CA, Flores TP, Taylor WR, and Thornton JM (1993) Identification and classification of protein fold families. Prot. Eng. 6:485-500.
30. Holm L, and Sander C (1994) Parser for protein folding units. Proteins 19:256-268.
31. Swindells MB (1995) A procedure for detecting structural domains in proteins. Protein Science 4:103-112.
32. Siddiqui AS, and Barton GJ (1995) Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions. Prot. Sci. 4:872-884.
33. Sowdahamini R, Rufino SD, and Blundell TL (1996) A database of globular protein structural domains: Clustering of representative family members into similar folds. Folding and Design 1:209-220.
34. Islam SA, Luo J, and Sternberg MJE (1995) Identification and analysis of domains in proteins. Prot. Engineering 8:513-525.
35. Murzin AG, Brenner SE, Hubbard T, and Chothia T (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540.
36. Holm L, and Sander C (1996) The FSSP database of structurally aligned protein fold families. Nucl. Acids Res. 24:206-210.
37. Gibrat JF, Madej T, and Bryant SH (1996) Surprising similarities in structure comparison. Curr. Opin. Struc. Biol. 6:377-385.
38. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, and Thornton JM (1997) CATH - a hierarchic classification of protein domain structures. Structure 5:1093-1108.
39. Pascarella S, Milpetz F, and Argos P (1996) A databank (3D-ali) collecting related protein sequences and structures. Prot. Eng. 9:249-251.
40. Overington J, Johnson MS, Sali A, and Blundell TL (1990) Tertiary structural constraints on protein evolutionary diversity; Templates, key residues and structure prediction. Proc. Roy. Soc. Lond. B241:132-145.
41. Levitt M, and Chothia C (1976) Structural patterns in globular proteins. Nature 261:552-558.
42. Holm L, and Sander C (1996) Mapping the protein universe. Science 273:595-603.
43. Holm L, and Sander C (1995) DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends in Bioc. Sci. 20:345-347.
44. Holm L, and Sander C (1997) Enzyme HIT. Trends in Bioc. Sci. 22: 116-117.
45. Madej T, Gibrat JF, and Bryant SH (1995) Threading a database of protein cores. Proteins 23:356-369.
46. Orengo CA, Jones DT, and Thornton JM (1994) Protein superfamilies and domain superfolds. Nature 372:631-634.
47. Bowie JU (1997) Helix packing angle preferences. Nature Structural Biology 4:915-917.
48. Chothia C, Levitt M, and Richardson D (1981) Helix to helix packing in proteins. J. Mol. Biol. 145:215-250.
49. Reddy B, and Blundell T (1993) Packing of secondary structural elements in proteins. Analysis and prediction of inter-helix distances. J. Mol. Biol. 233:464-479.
50. Russell RB, Saqi MA, Sayle RA, Bates PA, and Sternberg MJ (1997) Recognition of analogous and homologous protein folds: Analysis of sequence structure conservation. J. Mol. Biol. 269:423-439.
51. Rost B (1997) Protein structures sustain evolutionary shift. Folding and Design 2:S19-S24.
52. Brenner SE, Chothia C, and Hubbard TJP (1997) Population statistics of protein structures: Lessions from structural classifications. Curr. Opin. Struc. Biol. 7:369-376.
53. Chothia C (1992) One thousand families for the molecular biologist. Nature 357:543-544.